Core 2: Software Infrastructure for Network Models and Cell Maps

核心 2：网络模型和小区地图的软件基础设施

• 批准号: 10704622
• 负责人: Trey Ideker
• 金额: $ 7.74万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-14 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10704622
• 关键词: Biological; Cell model; Cells; Code; Computer software; Custom; Data; Data Analyses; Deposition; Development; Ecosystem; Elements; Environment; Generations; Genetic; Infrastructure; Lead; Libraries; Link; Maps; Ontology; Pathway Analysis; Proteomics; Publications; Publishing; Pythons; Research; Research Personnel; Resources; Scientist; Services; Software Framework; Software Tools; Visualization; Work; cancer cell; data dissemination; data exchange; data resource; digital object identifier; infrastructure development; network models; protein protein interaction; protein structure; public repository; repository; software infrastructure; tool; web app; web interface; web portal; web services; web site

CCMI v2.0 Core 2: Software Infrastructure for Network Models and Cell Maps Core Lead: Trey Ideker; Co-Investigator: Dexter Pratt SUMMARY The Software Infrastructure for Network Models and Cell Maps Core will support the CCMI Projects at all stages of research and publication. The core will provide infrastructure and assistance towards three main elements: (1) the Cytoscape desktop application along with tools and services from the Cytoscape Ecosystem; (2) NDEx, the Network Data Exchange; and (3) infrastructure for the development and deployment of web services and applications. First, we will support center investigators in use of the Cytoscape Ecosystem for analysis and visualization of biological networks, including protein--protein interaction networks from Project 1, genetic interaction networks from Project 2, and multiscale cancer cell maps from Project 3. The Cytoscape Ecosystem includes the well-known Cytoscape desktop environment, the HiView multiscale cell model viewer, the IQuery pathway analysis tool, multiple R and Python libraries, and the CDAPS software framework for the generation of multiscale cell models. Second, we will facilitate the use of NDEx by center investigators to publish CCMI cell maps, interaction data, and other products as “live” network data that can be immediately visualized and used. We will also provide assistance in the use of NDEx to share pre-publication network data between center investigators, including direct, programmatic access from Jupyter notebooks and other software. Third, we will provide assistance to Project 3 investigators in the creation of web interfaces and back-end services. For all projects, we will facilitate programmatic access to resources, hosting of websites, the use of Docker software containers, and the management of CCMI Github repositories. Finally, we will maintain and extend the CCMI web portal to provide access to (1) CCMI public networks and cell maps via the NDEx networks cloud, (2) CCMI software tools and resources, (3) custom websites and web applications CCMI v2.0

CCMI v2.0 核心2：网络模型和细胞图的软件基础设施 核心负责人：Trey Ideker;合作研究者：Dexter Pratt 总结 网络模型和细胞图核心的软件基础设施将完全支持CCMI项目 研究和出版阶段。核心将为三个主要方面提供基础设施和援助， 元素：（1）Cytoscape桌面应用程序沿着来自Cytoscape生态系统的工具和服务; (2)NDEx，网络数据交换;（3）用于开发和部署Web的基础设施 服务和应用。首先，我们将支持中心研究人员使用Cytoscape生态系统， 生物网络的分析和可视化，包括项目1中的蛋白质-蛋白质相互作用网络， 来自项目2的遗传相互作用网络和来自项目3的多尺度癌细胞图谱。Cytoscape 生态系统包括著名的Cytoscape桌面环境，HiView多尺度细胞模型查看器， IQuery途径分析工具，多个R和Python库，以及用于 多尺度细胞模型的生成。其次，我们将促进中心研究者使用NDEx发表 CCMI单元图、交互数据和其他产品作为可立即可视化的“实时”网络数据 和使用。我们还将提供使用NDEx的协助，以便在以下机构之间共享出版前网络数据： 中心调查员，包括直接的，编程访问从Xueyter笔记本电脑和其他软件。第三、 我们将协助项目3调查人员创建网络界面和后端服务。 对于所有项目，我们将促进对资源的编程访问，网站托管，Docker的使用 软件容器，以及CCMI Github存储库的管理。最后，我们会维持及扩展 CCMI门户网站，提供对（1）CCMI公共网络和通过NDEx网络云的小区地图的访问，（2） CCMI软件工具和资源，（3）自定义网站和Web应用程序CCMI v2.0